I dunno, if seeing him jack off to Asuka’s virtually naked body isn’t proof enough, I don’t really know what is. 
But go back and watch the series again. You can probly catch that Shinji really likes Asuka, and vice versa, the second time around.
woah woah end of eva came around cuz so many people thought the original endng sucked…tho now that you theasuka, ayanamie naked, jacking off thing… i hafta agree…tho its kinda weird to do that over someones body…